The role of Na+-coupled bicarbonate transporters (NCBT) in health and disease

Abstract

Cellular and organism survival depends upon the regulation of pH, which is regulated by highly specialized cell membrane transporters, the solute carriers (SLC) (For a comprehensive list of the solute carrier family members, see: https://www.bioparadigms.org/slc/ ). The SLC4 family of bicarbonate (HCO₃^-) transporters consists of ten members, sorted by their coupling to either sodium (NBCe1, NBCe2, NBCn1, NBCn2, NDCBE), chloride (AE1, AE2, AE3), or borate (BTR1). The ionic coupling of SLC4A9 (AE4) remains controversial. These SLC4 bicarbonate transporters may be controlled by cellular ionic gradients, cellular membrane voltage, and signaling molecules to maintain critical cellular and systemic pH (acid-base) balance. There are profound consequences when blood pH deviates even a small amount outside the normal range (7.35-7.45). Chiefly, Na⁺-coupled bicarbonate transporters (NCBT) control intracellular pH in nearly every living cell, maintaining the biological pH required for life. Additionally, NCBTs have important roles to regulate cell volume and maintain salt balance as well as absorption and secretion of acid-base equivalents. Due to their varied tissue expression, NCBTs have roles in pathophysiology, which become apparent in physiologic responses when their expression is reduced or genetically deleted. Variations in physiological pH are seen in a wide variety of conditions, from canonically acid-base related conditions to pathologies not necessarily associated with acid-base dysfunction such as cancer, glaucoma, or various neurological diseases. The membranous location of the SLC4 transporters as well as recent advances in discovering their structural biology makes them accessible and attractive as a druggable target in a disease context. The role of sodium-coupled bicarbonate transporters in such a large array of conditions illustrates the potential of treating a wide range of disease states by modifying function of these transporters, whether that be through inhibition or enhancement.

Keywords: Animal SLC4 gene evolution; Anion exchange; Bicarbonate; Chloride; Monogenic disease; NBCe; NBCn; NCBT; Na cotransport; SLC4; SLC4 structure; Sodium.

Figure 1.

Schematic of ion transport of NCBTs. A schematic showing the direction of ion movement for NBCe1/2 (green text), NBCn1/2/3 (red text), and NDCBE (blue text). Note: AE9, a relatively uncharacterized SLC4 family member, is referred to here as NBCn3.

Figure 2.. Structural comparisons of NDCBE, NBCe1, and AE1.

A. The structural superimposition of NDCBE (salmon), AE1 (gray) and NBCe1 (green) in the TMD. For clarity, all loops including EL3 are not shown. B1. AlphaFold prediction of monomeric NBCe1 (SLC4A4) 3D-structure, based on UniProt “Q9Y6R1.” The color coding indicates levels of similarity of known X-ray or cryoEN structures (ground truth: dark blue = >90; light blue = 70–90%; yellow = 50–70%; orange = <50%). Areas of known structure [1HYN (AE1 globular domain, Xray) [212], 6CAA (NBCe1, cryoEM) [79]] show >70% similarity, but still have areas of divergence in these structures as well as linker regions. B2. Dimer structure of NBCe1 [6CAA (cryoEM) [79]] connected to the globular domain of SLC4A1 (1HYN, Xray) [212] shown experimentally to be similar in human NBCe1 [33]. Dotted red lines indicate where linkers are which are not defined in any of the ground truth structures. EL3 is the major extracellular loop in the SLC4 family members, but is not defined in structures but rather only models.

Figure 3.. Ion coordination in NBCe1.

A structural model showing the region for coordination of Na⁺ (indicated by dashed purple line) and the region for HCO₃⁻ (indicated by blue dashed line) in the substrate pocket of NBCe1. NBCe1 has the capacity to bind two anions in the substrate pocket [204]. Material in panel A adapted from: ‘Wang et al., Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE, Nature Communications, published 2021, Nature Portfolio’ [199]. Creative commons licence can be found at https://creativecommons.org/licenses/by/4.0/ Material in panel B adapted from: ‘Wu et al., Molecular insight into coordination sites for substrates and their coupling kinetics in Na⁺/HCO₃⁻ cotransporter NBCe1, The Journal of Physiology, published 2022, The Physiological Society’ [204]. Licence number for reuse: 5687740758558.

Figure 4.. NCBTs in animals.

An overview of the distribution of NCBTs in the genome databases of various animal species are shown with the phylogeny of various vertebrate species based on the TimeTree database (http://www.timetree.org/) [97]. Tetrapods shown in blue section, teleosts shown in pink and orange, primitive fish shown in middle white section, mollusks shown in brown, insects, anilids and arthropods shown in green, and cnidaria shown in bottom white section. Open stars indicate the timing of three rounds of whole-genome duplication occurred in vertebrate evolution.